Why do I always have to re-render and re-connect project?!?

Question

Hoping someone can help me with what I imagine is a pretty basic issue...
Whenever I open my ProRes 422 HQ project, I always see two problems:
(1) I get a warning that 160 audio files need to be reconnected
(2) About 20% of my timeline requires rendering for video and audio
Neither of the above is a problem in and of itself. I simply reconnect the audio files and render out the unrendered timeline sections.
I then SAVE my project and work normally. And of course I SAVE again just before I quit for the day (in addition to frequent auto-saves).
But the next day, when I boot up my Mac and re-open the project, I still see the above two issues! I then have to reconnect media AGAIN and render the same sections AGAIN! Never fails.
How come these changes never get saved? What can I do to ensure that these items get saved? The reconnecting media is not a big deal but the re-rendering takes an hour.
Any input appreciated.

Answer 1

Could be a system/os problem or might be a corrupt sequence or project in fcp.
Simplest thing to do, create a new sequence with the same settings and copy everything from the old sequence to the new. 
Still have the same problem?  Try copying your sequence to a new project.
As a test, you might try changing your render scratch disk to your startup drive as a test and see if the problem persists.
Make sure your esata card's drivers are up to date.
Are you absolutely positive all clip settings match the sequence settings?  Could be a slight difference in audio sampling or someting of the like causing the need to render certain clips.  Is it the same clips that always require rendering.  Put the playhead on a clip in the sequence that requires rendering and match frame (f) and edit into a new sequence.  When fcp asks if you want to match sequence settings to clip, say yes.  Does it require rendering?  If not, there must be some difference between the clip settings and the original sequence settings.